MetNetComp Database [1] / Minimal gene deletions Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : ctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b2242 b1478 b0474 b2518 b1241 b3831 b4069 b1278 b3752 b3926 b2297 b2458 b2779 b2781 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b3908 b1656 b1759 b0937 b4161 b0261 b2799 b3945 b1602 b4138 b4123 b0621 b2913 b4381 b2406 b0452 b0529 b2492 b0904 b3825 b3028 b1380 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.320799 (mmol/gDw/h)
  Minimum Production Rate : 0.640478 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.044519
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.386034
  EX_pi_e : 2.230879
  EX_so4_e : 0.080784
  EX_k_e : 0.062618
  EX_fe3_e : 0.005152
  EX_mg2_e : 0.002783
  EX_ca2_e : 0.001670
  EX_cl_e : 0.001670
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000222
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 51.045718
  EX_co2_e : 35.367259
  EX_h_e : 6.414469
  EX_ac_e : 1.152980
  EX_succ_e : 0.805004
  Auxiliary production reaction : 0.640478
  EX_3hpp_e : 0.058224
  EX_glyc_e : 0.000158
  DM_5drib_c : 0.000072
  DM_4crsol_c : 0.000072

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

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Last updated: 21-Sep-2023
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